In order to understand the development and functioning of the thymus, both in terms of T cell differentiation and stromal cell environmental support, we have undertaken a molecular approach to identify genes that are uniquely expressed in this organ. Several strategies are currently being explored to accomplish this goal. One is to make cDNA libraries from fetal thymic organ cultures treated with deoxyguanosine and anti- CD45 to remove T cells and other hematopoietic cells. Subtractive hybridization approaches are then undertaken to further enrich for stromal cell cDNAs specific to the organ. The remaining cDNAs are then sequenced to identify new genes. Novel cDNAs are in turn tested by Northern Blot analysis and in situ hybridization to check for selective expression in thymic stromal cells. Although this project is still in its early phases, we have already sequenced 288 cDNAs and identified 182 with novel sequences. Two of these appear to be expressed in a thymic cortical epithelial cell line and not in a thymic medullary epithelial cell line. The full sequences of these two cDNAs are now being determined and detection of their expression in thymic sections by in situ hybridization is underway.